Variant report

Variant	rs11668617
Chromosome Location	chr19:18746522-18746523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18738729..18743227-chr19:18745299..18749316,6	K562	blood:
2	chr19:18699138..18701400-chr19:18744196..18746923,2	K562	blood:
3	chr19:18745231..18747115-chr19:18793241..18795774,2	MCF-7	breast:
4	chr19:18703681..18707981-chr19:18746387..18750076,5	K562	blood:
5	chr19:18716807..18719687-chr19:18745756..18748857,3	K562	blood:
6	chr19:18681409..18685264-chr19:18744559..18747664,3	MCF-7	breast:
7	chr19:18739642..18741715-chr19:18744659..18746767,2	MCF-7	breast:
8	chr19:18704018..18706684-chr19:18745467..18747163,2	MCF-7	breast:
9	chr19:18681104..18684544-chr19:18745683..18749906,4	K562	blood:
10	chr19:18698512..18700358-chr19:18745222..18750244,4	K562	blood:
11	chr19:18698708..18701515-chr19:18746316..18749182,4	MCF-7	breast:
12	chr19:18740493..18743219-chr19:18745834..18748100,2	K562	blood:
13	chr19:18744967..18748846-chr19:18753096..18757449,4	MCF-7	breast:
14	chr19:18744815..18748522-chr19:18792822..18794594,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000263490	Chromatin interaction
ENSG00000105662	Chromatin interaction
ENSG00000006016	Chromatin interaction
ENSG00000167487	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000221983	Chromatin interaction
ENSG00000105696	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10402536	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10403231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10423102	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs10423271	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10423676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10423852	0.87[ASN][1000 genomes]
rs1076234	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1076235	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11085237	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11085239	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12052075	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12459017	0.83[AMR][1000 genomes]
rs12610845	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12974161	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12974777	0.87[ASN][1000 genomes]
rs12976741	0.84[ASN][1000 genomes]
rs12980154	0.84[CEU][hapmap];0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs12983476	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1473115	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2014914	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2238647	0.89[CHD][hapmap];0.81[JPT][hapmap]
rs2283617	0.86[CHD][hapmap]
rs34143665	0.87[ASN][1000 genomes]
rs34190814	0.91[ASN][1000 genomes]
rs3795026	0.96[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4808146	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808841	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4808842	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71332133	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7249956	0.91[CHD][hapmap];0.82[JPT][hapmap]
rs8110573	0.91[CHD][hapmap];0.82[JPT][hapmap]
rs889362	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs889363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	esv3332947	chr19:18745902-18749700	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11668617	UBA52	cis	lymphoblastoid	seeQTL
rs11668617	CRTC1	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18725600-18747200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr19:18729400-18747200	Weak transcription	Brain Angular Gyrus	brain
3	chr19:18740600-18746600	Weak transcription	Fetal Brain Female	brain
4	chr19:18740800-18746600	Weak transcription	Brain Anterior Caudate	brain
5	chr19:18740800-18746600	Weak transcription	Brain Substantia Nigra	brain
6	chr19:18740800-18747200	Weak transcription	Brain Hippocampus Middle	brain
7	chr19:18740800-18747200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr19:18741200-18746800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:18741200-18747200	Weak transcription	Adipose Nuclei	Adipose
10	chr19:18745200-18746600	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr19:18745600-18746600	Enhancers	Duodenum Mucosa	Duodenum
12	chr19:18745600-18746600	Enhancers	Esophagus	oesophagus
13	chr19:18745600-18746600	Enhancers	Fetal Lung	lung
14	chr19:18745600-18746600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr19:18745600-18746600	Bivalent Enhancer	Placenta	Placenta
16	chr19:18745600-18746800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr19:18745600-18746800	Enhancers	Right Ventricle	heart
18	chr19:18745600-18746800	Flanking Active TSS	HepG2	liver
19	chr19:18745600-18747000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr19:18745600-18747200	Enhancers	Primary T cells fromperipheralblood	blood
21	chr19:18745600-18747200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:18745600-18747200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr19:18745600-18747200	Enhancers	NHEK	skin
24	chr19:18745600-18747800	Enhancers	Fetal Brain Male	brain
25	chr19:18745800-18746600	Enhancers	Right Atrium	heart
26	chr19:18745800-18746800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:18745800-18746800	Enhancers	Primary hematopoietic stem cells	blood
28	chr19:18745800-18747200	Enhancers	Primary T cells from cord blood	blood
29	chr19:18745800-18747200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:18745800-18747200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr19:18745800-18747400	Enhancers	Stomach Mucosa	stomach
32	chr19:18746000-18746600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
33	chr19:18746000-18746600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:18746000-18746600	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr19:18746000-18746600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:18746000-18746600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr19:18746000-18746600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:18746000-18746600	Enhancers	Gastric	stomach
39	chr19:18746000-18746600	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr19:18746000-18746800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
41	chr19:18746000-18746800	Enhancers	Brain Germinal Matrix	brain
42	chr19:18746000-18746800	Enhancers	Thymus	Thymus
43	chr19:18746000-18747000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:18746000-18747000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr19:18746000-18747000	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr19:18746000-18747200	Enhancers	Primary B cells from peripheral blood	blood
47	chr19:18746000-18747200	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr19:18746000-18747200	Enhancers	Fetal Intestine Small	intestine
49	chr19:18746000-18747200	Weak transcription	Left Ventricle	heart
50	chr19:18746000-18747200	Weak transcription	Lung	lung

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